General information for g2967.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U5 small nuclear ribonucleoprotein 40 kDa protein.
Parent gene
- The parent gene g2967 is located on chr_3: 21622217..21623088 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g2967 | g2967.t3 | TSS | g2967.t3 | 21621293 | 21621293 |
| chr_3 | g2967 | g2967.t3 | isoform | g2967.t3 | 21621361 | 21623088 |
| chr_3 | g2967 | g2967.t3 | exon | g2967.t3.exon1 | 21621361 | 21621589 |
| chr_3 | g2967 | g2967.t3 | cds | g2967.t3.CDS1 | 21621361 | 21621589 |
| chr_3 | g2967 | g2967.t3 | exon | g2967.t3.exon2 | 21621756 | 21621910 |
| chr_3 | g2967 | g2967.t3 | cds | g2967.t3.CDS2 | 21621756 | 21621910 |
| chr_3 | g2967 | g2967.t3 | exon | g2967.t3.exon3 | 21621988 | 21623088 |
| chr_3 | g2967 | g2967.t3 | cds | g2967.t3.CDS3 | 21621988 | 21621990 |
| chr_3 | g2967 | g2967.t3 | TTS | g2967.t3 | 21623081 | 21623081 |
Sequences
>g2967.t3 Gene=g2967 Length=1485
ATGATTTCGAGTGCCCAAAAGAGACCTGGTGATAATCTGAGTCTAGTTGCTGTTCAACAG
AATACTAAAAGAGCTCGAAATGATGAATTGGTGGCGACTTTTAAAGATAAACAACTTATG
GAAAAAGGAATTAACAGAACATCAAATCTTTATGCACCTATAATGAAACTAGAAGGGCAT
GAAGGAGAAATATTCTCTTGTGAATTTCATCCAGAAGGCGAGTTACTTGCATCAGCCGGT
GTTGAAAGAAAAATATTCTTATGGACTGTATATGATGAGGAATGTCAAAATATTGCAGTC
ATGAGTGGACATAAAGGAGTTATTACCGAAATGCATTTTAGTCCTGATGGAACTTCAATT
TATAGCTGCAGTACTGATAAGTTTTAACGCAAGAAGAGGGGTTGAGACTTTAGTAACAGG
AAGTGATGATAACACGATTAAAATTTGGGATGCACGTAAAAAACTTGTATGTCACACCCT
CGAAAGCAATTATCAAGTAACTGCTGTTTGCTTAAATGACACAGCTGAACAAGTGATAGC
AGGCGGTATTGATAATGATATCAAAATTTATGACATTAGAAAGAACGAAATATTGTTTAA
AATGCAAGGTCACACTGATACAATTACTGGTTTAAAATTATCTCCATGTGGTTCATATGT
TCTTTCAAATTCGATGGATAACACTTGCAGAATTTGGGACATTAGACCATATTGTTCACA
AGATCGATGTAAATCAGTTTTTCAGGGACATTCCCATAATTTTGAGAAAAATCTTTTAAG
ATGTGCATGGAGTTCAGATGGCACAATGATTTCAGCTGGATCGGCGGATAGATTTGTTTA
TATTTGGGACGTTAATTCTAAGAAGATTCTATACAAACTCCCTGGTCATTTAGGAGCTGT
AAATGATGTTGATTTTTCACCAAAAGAAGAAATTATTCTCAGTGGTTCTTCAGATAAGAC
TCTATACATGGGTGAATTACTAGAAAATTAGATTGCTATCTTTCTTTCTTATCTCATTTT
TGTTATCGCTCTCAAACCATTTTTAAGTACTGTATTTAAAATGAAGCGAAAATAAATTAT
CATCTGCTGAAAAGATCAACAATCCTAATGAGAATATAAAGAAGATAAGAACTACGCACT
TTTATCCTTCTTTGAAACATTCGTCATCAGTATGAAGAGAAATGTGACGTCAAGTTATTA
CCATCTACGTAGGCATCACTTTATTTTGAGCGTAATACCATAAACCTTTCCTATATTTAG
TCCTATAGATATATAATTTCATTTGAAAGAAAGAAAAAAATGTTTAACGAGAGAGTGAAG
AATAAATATACGAGAGCAACATTTAATATGCGAGAGTTAAAAATAAAGAATGAGAGTAAA
AGAATATGATACCGACTTCTCTCTTTTCATGTCATGTTATGAGAAAGGAAGATATTTGTC
ATATACAGTTTAAGTGAAATAAATTCTACTCTGAAGAGAAGAAAA
>g2967.t3 Gene=g2967 Length=128
MISSAQKRPGDNLSLVAVQQNTKRARNDELVATFKDKQLMEKGINRTSNLYAPIMKLEGH
EGEIFSCEFHPEGELLASAGVERKIFLWTVYDEECQNIAVMSGHKGVITEMHFSPDGTSI
YSCSTDKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2967.t3 | Gene3D | G3DSA:2.130.10.10 | - | 3 | 128 | 0.0000000 |
| 3 | g2967.t3 | PANTHER | PTHR44006 | U5 SMALL NUCLEAR RIBONUCLEOPROTEIN 40 KDA PROTEIN | 27 | 127 | 0.0000000 |
| 2 | g2967.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 53 | 88 | 0.0001800 |
| 1 | g2967.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 96 | 127 | 0.0011000 |
| 8 | g2967.t3 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 57 | 128 | 16.8760000 |
| 10 | g2967.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 57 | 98 | 12.4130000 |
| 9 | g2967.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 101 | 128 | 8.8710000 |
| 6 | g2967.t3 | SMART | SM00320 | WD40_4 | 50 | 89 | 0.0000021 |
| 5 | g2967.t3 | SMART | SM00320 | WD40_4 | 94 | 128 | 3.2000000 |
| 4 | g2967.t3 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 53 | 127 | 0.0000000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
